From Shadows
by Short Angel
Summary: AU Mulder finds his sister, but she's not the sister he expected. Meanwhile both agents find out that Scully's more than she seems, and is causing panic among the conspirators.
1. Chapter 1

**Author's Note:** The T rating is just to be on the safe side, and I stink at summaries so be assured the story will be better than the summary.

**Summary/Disclaimer:**

Mulder gets a new informant who holds a few secrets and a few suprises for him. All of which leads him into a whole new conspiracy. MSRNone of these characters are mine, they belong to Chris Carter and the talented people who brought them to life; Gillian Anderson and David Duchovny.

Mulder walked through the empty warehouse, his latest informant had provided information that a folder on his sister could be found at the warehouse. He peered at the dust covered crates that lined the wall, half expecting a Syndicate member to reveal themselves from shadows, though the moon was illuminating much of the warehouse. In the center of the room was a single crate with the file in question sitting a top it.

Mulder's fingers shook as he opened looked at the name on the tap at the top: _Mulder, Samantha_. On the cover of the folder was a note, but Mulder was too busy leaving the warehouse, and too excited with this find to notice it.

_Mulder,_

_You have no idea how it hurts to write this- but the sister you have searched so long for isn't going to return to you. The contents of this folder will reveat something my associates have hidden from you for so long. The information in here is highly classified so I beg you to take care._

TBC


	2. Chapter 2

Two women watched Mulder's retreating back, "I can't do this anymore," the shortest of the two sighed as she spoke, "give him false hope that his sister that he spent most of his life searching for will come back to him."

"I thought that was why you gave him the papers in the first place," the other woman was slightly taller and sounded much older. She glanced at the other woman as she nodded, "But that isn't the only thing that is bothering you is it Dana?"

"You are too perceptive old timer," Dana began to walk away, her black, knee length coat trailing behind her.

"After spending so much time, helping you grow, you tend to know when something's wrong with your charge."

Dana stopped, "I'm tired," she gestured to the warehouse, " of this meeting in secret and in shadows. Of the hidden agendas."

"Aren't we all?"

"Even you Ana? I thought you lived for this life."

"Even your tough-as-nails mentor. You are smart Dana, you never got involved to the point where you couldn't get out. You didn't let them brainwash you, unlike Samantha Mulder. Through it all you never forgot you were Dana Scully."

"It just seems like I've been fighting Them my whole life."

"You have, ever since you were six. Until the war is won..."

"...we must all fight our battles. I know it by heart Ana."

"About Mulder, Dana... tell him. He deserves to know," Ana walked away leaving Dana open mouthed in shock, "just let me know how it turns out."

TBC


	3. Chapter 3

Outside the warehouse the rain had begun to fall hard. Dana began to walk back to her apartment in the moonless night, she had no worries of any attack despite the fact that the neighborhood was bad. The only thing that kept her dry from the downpour was her jacket, but the cold rain didn't effect her, little did.

_Sure Ana, he'll understand. Understand that his partner is a freak of nature, an experiment that went wrong as far as her creators are concerned. My own family didn't understand, it was only my father who kept me from being thrown out, so yeah of course he'll understand, _she thought bitterly.

She walked through the park near her apartment, her hair sticking to her face; her make-up was beginning to run down her face. She sat down heavily on a nearby bench. _How do I even begin to tell him anyway? _She could just see the conversation now:

"_Mulder, there's something you need to know about me."_

"_What?"_

_A sigh, "During the Cold War the government began to experiment on children, trying to develop a supersoldier to fight in the war. They recruited the top doctors, even enemy doctors to achieve their goal. They gave them telepathic abilities, increased agility and strength. Heightened intelligence, among other things_."

"_Like the Eves?"_

"_Yes, but these were successes. My father was recuited to transport the scientists that participated in the project; he wasn't told what they were doing, just that it was to help save mankind. Ever the man bound to duty he agreed..."_

"_Until he found out what they were up to."_

"_Yes, and then he was punished... by being forced to watch me undergo the experiment."_

Scully laughed aloud at how corny the whole thing sounded. The information may have be serious, but who would believe it. Perhaps it was the only way that the Syndicate could assure themselves that their true plans would never be revealed. Make them so only the crackpots would believe and spread the word, then again Mulder was far from a crackpot.

"Maybe you should give us "crackpots" the benefit of the doubt with your secrets."

**Author's Note: **Thanks for the reviews. The idea for Scully's situation was kind of inspired by the Dark Angel TV series. I know this chapter was short, but I promise they'll be longer next time.


	4. Chapter 4

Scully whipped around, "Mulder!" He took a seat next to her, looking lower than Scully had seen him in the entire time she's known him, "How long was I broadcasting?"

"For pretty much for all of it...So you're an advanced sort of human being created by Them with alien technology? And my sister is just like you, and not coming back?"

Scully nodded, "I'm so sorry Mulder. I never wanted you to find out like you did about her, but there was no other way." Mulder wouldn't look at her, just sat there silent, "Say something Mulder, anything." Scully was begging.

"And how did you figure I'd find out about you?"

"I was trying to figure out how to tell you, in person-" Mulder stood and began to walk away into the rainy night, "Mulder-"

"I just need some time to think about all this Scully."

Scully watched him go, though her mind screamed at her to go after him, she could feel her tears blending into the rain.

A week passed, neither Mulder or Scully made any attempt to contact one another. Both of them were too hurt by the other to make the first move.

Meanwhile the Syndicate was celebrating what seemed to be Mulder's downfall. The spirit of his quest seemed to have been broken at long last, and the higher ups had sent congratulations to Dana for finally achieving the goal.

Ana was growing increasingly worried every time the redhead glanced at her with sorrowful blue eyes. Something was majorly wrong, and had to be set right. One evening she found Dana glaring at marking on her right wrist, "Dana," she approached her like one who was trying to help a hurt and frightened deer. "What's wrong."

"He wasn't ready Ana, and he found out in the worst possible way."

"What happened?"

"I was remembering all the things that happened when I told the people I care about in the past, and was trying to figure out how to tell him. I honestly believed he would be different, but he was near and he heard because I was broadcasting."

"Oh child," she drew Dana in her arms.

"It's over," Scully broke away, and began to walk away, tears shining in her eyes, unshead. Ana decided she needed to take action.

Mulder was staring at some corny, fake porno he had put in the VCR, not really watching the screen. His entire world had been lost in one day, and he had spent the last week feeling entirely lost.

_Samantha, Scully _; he didn't know which truth hurt worse.

"Both, though perhaps Dana's a bit more," said a voice.

Mulder turned fast, gun in hand, "Who the hell are you and how in the hell did you get in here?"

"She hurts just as much you know. You confirmed her worst fears, everyone besides her father has abandoned her when they learn the truth. Though she and her mother are on better terms right now. That's why she didn't tell you what she was. And you hurt because she didn't trust you."

"Who are you, tell me or I'll shoot Dammit!"

"Gun's don't phase me anymore Mulder, I'm Ana. You could say I'm Dana's mentor when it comes to fighting the conspiracy. Dana's hurt Mulder, she didn't want it to come between the two of you."

"And I'm letting it," Mulder let the gun drop to his side.

"She's in the usual spot, go talk to her."

Mulder didn't need told twice.

**A/N: **TBC Reviews are most appreciated!


	5. Chapter 5

**Author's Note: So sorry I haven't updated in a while, I've started school so who knows when my updates will be, but I will update when I get the chance. **

**This chapter starts some telepathic communication between Mulder and Scully; the code is as follows: _italics _Scully_, -italics- _Mulder. Now on with the show:**

Scully sat heavily on the bench, but it wasn't just any bench, it was their bench.

_Why did I come here? I am trying to forget him._

_Because you don't want to, _a voice nagged at the back of her head.

_Shut-up._

Scully tried to keep her tears in check, looking down she turned her right wrist. The tattoo that was there was some sort of an id in the ancient language the Greys spoke.

_-Scully-_

_I'm going to kill Ana, _she directed the thought to herself.

_-I can hear that you know.-_

_Go away Mulder, I'm not in the mood_.

_-I just want to talk, face to face.-_

_You seem to have no trouble this way._

_-Suit yourself... Ana, your friend stopped by. She knocked some sense into me, about why I was so upset. Not about the truth about Samantha, but about you.-_

_Why me, _Scully couldn't hide her interest.

_-Because you didn't tell me - you were so hurt by the people you loved when you told, and didn't want to go through that again. Just like I did. -_There was a note of shame in his voice.

_Now he notices._

"I just wanted to apologise." Scully just stared at the water for a few moments, "Please forgive me."

_I can never stay mad at you, _she shook her head. "How do you do it? No matter how pissed I get at you I can never stay mad."

"It's one of my charms."

Scully stood and walked over to Mulder and pushed him, "So I was wondering Scully, when did you become a ... hybrid, for lack of a better word."

"When I was six..." Scully broke off turning around suddenly.

"What is it?"

"Mulder hide in the bushes and don't move." Mulder looked like he wanted to argue, "Samantha's near and I'm not about to let her tear you limb for limb,"

Mulder climbed reluctantly into the bushes, and Scullywhispered after him, "And don't for any reason use the stone Mulder, she'll know."

Mulder could hear the fear in Scully's voice, ashard as she tried to hide it.


	6. flashback

_A sixteen year old Dana Scully stood in the playroom of the underground bunker. All around her were other children like herself, playing with one another, and trying out their new abilities. In the corner sat a brown haired girl about the same age as Dana, on a makeshift throne surrounded by girls who were bringing her food, and their valuable possessions. She looked at the items bored_, _then stormed off._

"_What's her problem?"_

"_Must not be pleased with her followers," she turned to face the brunette beauty that was Sapphire._

"_Must not be. Then again she's never pleased until she has that chain smoking son-of-a-bitch waiting on her as well," Sapphire's sapphire eyes darkened, "I thought I told you to get out of this."_

"_And Ana, and Ahab. I can't let this happen to anyone else Sapph_."

"_Typical Dana, always noble."_

"_Besides Spender wants me to discredit her Bitchiness' brother_. _Not that I will, to be honest I got the impression that he was actually all right."_

"_Dana," called Ana._

"_I'll be right back_."

_Dana walked over to Ana and Ahab, who looked about ten years older than they were. The stench of smoke hung in the air, and Dana could see the trail of smoke hanging in the air all down the hall, "What's up?"_

"_They forced us to give in Dana," said Ana sadly._

"_How?"_

"_He threatened to kill both Missy and you Starbuck," said Ahab defeated._

"_Well, then I just won't discredit him."_

_Dana walked back into the playroom, to deliver the bad news to Sapphire. There was a crowd in the center of the room, "What's going on?" The little girl looked up, "Sapphire and Samantha got into it."_

"_Sapphire!" Dana called trying to reach the center of the crowd and the fight without much success._

"_GO DANA JUST RUN! SHE KNOWS! THEY KNOW! THEY K--"_

_What exactly They knew Dana never found out as Sapphire crumbled to the ground unconscious, and Samantha turned to attack Dana. For once in her life, taking Sapphire's advice, Dana ran out of the room, heading for theexit,all the while feeling guilty for leaving Sapphire behind._

_Behind her she could hear Samantha pursing her;yelling at her,the comments fell on deaf ears. Dana ran for her life, not listening,she ducked around the corner and watched Samantha run by. Tears silently flowed down her face, as her knees gave out and she sunk to the floor, which was were Ana found her an hour later. _


	7. Chapter 7

**Thanks for all the great reviews, keep them coming. Okay, okay I hear you people : you want longer chapters and I'm willing to oblige, or at least try to. I can't guarantee I'll succeed, but what can you do - I have to hold your interest somehow - lol. **

* * *

Scully stood facing Samantha, she could hear her heart racing. Samantha was the strongest, and who knew what she was capable of, "Still worried about the innocent? Those weak and pitiful fools who have no idea of the great honor they'll have when the invasion starts and they are taken host."

"Still the same, after all this time Samantha ... blood thirsty ... angry ... didn't you get enough when you took out Sapphire?"

"Sapphire? Ah yes ... she sends her love; but not to worry, you and that idiot I have to call my brother will be joining her shortly." Samantha reached behind her and puller out an antique looking knife, holding it at arms length away from her body.

Scully's whole body tensed, "If there is one thing I'll never get about Mulder it's how can he still care about you. You don't care about no one but yourself and the Project. I have to remind myself that he doesn't know your true nature."

"I'm only forced to call him my brother by blood just like he is forced to call me his sister."

"That's just it, he doesn't see it that way. To him, you'll always be the eight year-old sister he loved, and remembers. And inside him still burns the hope that you'll return as like that eight year-old, just older."

"Love is that it? Love is weak, a wasted emotional space that can be used for so much more. Perfect for humans and traitors like you, but not for us superior beings."

Mulder was itching to go beat this woman, even if she was his sister. No one called Scully a traitor or anything of that nature without getting their arse kicked by him. Samantha suddenly looked away behind her and back at Scully in a split second with the maniac gleam in her eyes, without warning charged at Scully, the knife slashing at her upper arm.

"Ahhh," Scully winced turning and clutched at her now bleeding arm. Samantha just kept running. Mulder ran out of the bushes the second Samantha was out of sight. "Scully..."

"I...fine Mulder, just hurts like hell. I'll heal soon though not to worry."

Mulder didn't look convinced, but didn't say anything, "So where did she go?"

"Probably to hide in the shadows again."

* * *

**A week later**

Scully walked through the semi-empty parking garage. The only sound was the clicking of her heels on the pavement. As she neared her car she saw a figure hunched over beside the driver's side door.

"Sapphire!" she rushed over to the figure, who looked up weakly.

"I thought I told you to get out of this mess."

"Well you know me, can't keep out of trouble if my life depended on it."

Scully pulled Sapphire up to her feet. Sapphire shook her head, "Even so I would have thought that you'd have more sense than to beat Samantha Mulder in the middle of her brother's apartment building. None the less right in front of his apartment. She could have killed you."

Scully brushed it off, "I'm fine, besides, you should have seen her."

"I did. You did one hell of a number on her Dana.," color rose on Scully's cheeks, " The only reason I'm even standing here is because you bruised her and Their ego. I've been her punching bag, and if I was a good one, and took my beating without complaint I got to go into for upgrades."

"Lucky you."

"Hey are you still a part of that rebellion?"

"Yeah why?"

"Well let's go talk that partner of yours, and I'll explain it to both of you at once."

"You just want to meet Mulder who are you kidding."

"Not you obviously."

* * *

**Mulder's Apartment**

"Mulder it's me. Let me in."

Mulder stood on the other side of the door with Samantha behind him; her knife in hand.

"Unlock the door big bro. Then step back."

Mulder walked towards the door, Samantha pressing the knife into his back. He had the stone in his pant's pocket, he wanted to contact Scully with it, but knew Samantha would have been able to tell. He unlocked the deadbolt and then stepped back, "The chain too." Mulder obliged as she caused the knife to press into his back a little bit further.

Samantha pulled him close to her as soon as the door was unlocked, angling the knife so the blade pressed against his neck. The knob started to twist; it must have beena bit too slowly for Samantha's likingbecause she ripped open the door telepathically, almost ripping it from it's hinges.

The doorway was empty, "WHERE IS SHE!" Samantha demanded, Mulder looked at the madwoman, Scully and another woman were standing right there in plain sight. Scully looked at him andshook her head as Mulder opened his mouth to say something.

Samantha pulled him out into the hall past where they were, suddenly she stopped, "I don't think so," she pushed out with her mind, causing Scully and Sapphire to slam into the wall andcrumble to the ground now visible to both. "Noooo," Mulder moaned softly.

"THOUGHT YOU COULD HIDE HUH? THOUGHT YOU COULD TRICK ME!" Samantha yelled at their prone bodies, she pulled Mulder away, "Don't worry bro," she said in a fake reassuring voice, "they'll just have a headache." Smiling she pulled Mulder toward the elevator.


	8. Emily

_Mulder's Apartment_

_A few hours later_

Sapphire rolled over onto her back, groaning softly. Her head felt like she had the entire percussion section of an orchestra playing there. Slowly she let her head turn to the left a little, she could see the door still hanging by a hinge on the inside of the apartment, the broken hinge laying right next to her head. Inside the apartment she could hear someone banging things around, as her head began to clear.

"Dammit!" Dana stormed out of the apartment, Sapphire pulled herself into a sitting position, Dana nearly stepped on her, "Watch it," yelped Sapphire. "Sorry," muttered Dana absentmindedly, walking toward the elevator.

Sapphire jumped to her feet, following her friend, "Where are you going?"

"To find him."

"Not alone you aren't! Samantha is way too powerful to take on alone."

"You're welcome to come with, but I'm not wasting anymore time."

Sapphire had to run to catch up with the shorter woman, as she impatiently punched the elevator button, "Okay Dana, but we'll need help. There's a group, it's not as high profile as yours. It sabotages Them from within, but it's never had enough manpower to make a big move."

"So where is this group located?"

"In the old underground bunker. I met their leader Leki when I was being used a punching bag. She practically saved me."

"Let's go then."

* * *

_Underground Bunker_

_Five hours later_

The two women walked through the dark, dusty hallways of the abandoned, underground bunker. Dana shivered as they walked past the playroom, "I've never been here since that day."

"Really?"

"Yeah, and I hoped I'd never had to see this place again. This was where my entire life was planned out for me, without me even having a say."

"You mean they planned for you to become a doctor?"

"Yeah, so I'd have the qualifications to discredit Mulder."

A soft voice from the shadows interrupted their discussion, "Who is there?"

"It's me Leki, I have Dana with me."

A woman stepped into the light, being created by a nearby small window, "Greetings Sapphire."

Dana stepped back, and softly gasped, then seemed to have lost her voice. The woman was tall, about 5' 8" with long black hair. She looked normal in all ways except for the cat's eye that was in the middle of her forehead, right above her normal eyes. All three eyes turned toward her, "Hello Dana, I'm Leki."

Dana quickly recovered her voice, "Hello. I'm sorry for staring, it just shocked me that's all." She was embarrassed for losing her control, momentarily.

"It's quite all right. I am one of the first of us, and it seems when they created me they couldn't decide if we should have two or three eyes. I'm glad they decided to stick with two."

"Me too," agreed Sapphire.

Leki and Dana laughed, suddenly they heard little feet running up the hallway behind Leki. A little girl about five or six rushed past Leki at Dana, wrapping her arms around her, "Mommy!"

Dana paled, her mouth moved, but no sound came out. "Emily?" she finally managed.

"I missed you Mommy. I love you."

Leki spoke up, "The Emily you saw die was a super soldier clone. It was never meant to be seen outside the complex. This is the real Emily."

Dana bent down wrapping her arms around the little girl, "I love you too Emily."

* * *

_Syndicate Complex_

_Right outside Washington D.C._

Samantha dragged her brother into a cell, "Wait here and I'll be back soon bro." She gave him a small peck on the cheek, then turned to leave. Smiling, she shut the door with a loud clang. Mulder could hear the lock clicking into place. Mulder reached into his pocket where the stone was. He wanted to contact Scully, tell her where he was, and that he was safe, but he knew Samantha would be able to track it. It wasn't a risk he was willing to take, for now he would just wait for Scully, and hope that all she had gotten from Samantha was a headache.

Samantha walked toward CSM still smiling in her victory. CSM frowned when he saw her coming, his adopted daughter was often to rash in her actions. "You did it didn't you?"

"Of course. He's here right now."

"Fool. Scully won't stop until she get's him back."

"She needs to pay for what she's done to you father, to the Project. Besides we know she's no match for me."

"You're wrong, though we've upgraded you, it seems Dana has somehow gotten even stronger than you, my daughter. If you were to fight, she would win."

"Then upgrade me again so I can win."

"There are no available upgrades at the moment. We have put all we can into you."

"Then how can SHE be stronger!" Samantha slammed her fist into the wall besides CSM, barely missing him.

"Her body is adjusting her abilities to her needs. Facing you has made them stronger."

"I don't care, upgrade me when they become available. My so- called brother stays here, I want to beat her." She stormed away, CSM looking fearful for the first time in his life. An underling approached him, "Sir?"

CSM turned to him, "She will never beat Dana Scully. I fear the ultimate project,and the result of our hard work will soon be no more."

TBC

Please Review


	9. Explanations

**Part 9 - Explanations**

**Author's Note: Sorry it's been so long since I've posted last. I've been busy with school and got caught up in another story I was doing. I'm back at it now, so hopefully my posts will be less further apart. **

Sapphire and Scully sat at a large table that had been set up in the middle of the what once was the playroom. Across from them Leki stood, watching as Emily climbed up into her mother's lap.

"How is this possible? We can't have kids, They made sure themselves." said Sapphire.

Leki smiled gently at the younger woman. "You see Sapphire, Dana is not like the rest of us. Just as Samantha is not like the rest of us."

Scully looked at her. "I'm different? How?"

Leki pushed a button on the side of the table causing a screen to drop down. An image was projected on it of a DNA strand. "This is Dana's DNA, and next to it," another image was projected along side the first, "is yours Sapphire. You'll notice the differences in the areas that control strength, and reproduction ... along with several others."

"The only one of us They made differently was Samantha. So how is this possible?" asked Scully, staring wide-eyed at the screen.

"Your abduction, which was punishment for helping Mulder, it had a unforseen result. Whatever tests, or "improvements" they made to you then unwittingly undid what They had worked so hard to do in the first place."

"You know one thing I've never understood is that They want to make an army of us right?" said Sapphire, the other women nodded. "So why make us infertile? Don't They want us to make more, so Their army grows?"

"They probably want to control it as much as possible." said Scully, hugging Emily a little tighter. The little girl had fallen asleep in Scully's arms while they had talked.

Leki nodded, "That is our guess as well. However, that's not all that was done-"

"There's more!" said Sapphire.

"Yes, you see what They did, also made Dana's body adjust to the new situations it is put through such as-"

"-The fight with Samantha, that I won." Scully finished.

Leki nodded. "You are now stronger than any one of us. Including Samantha Mulder."

Scully stood and set the sleeping Emily in the chair next to her. "I can't believe this."

"Believe it, you would've have been able to win otherwise." said Sapphire.

Scully just stared at the screen before her, and then dropped to the floor in a dead faint. "Dana," both Leki and Sapphire shouted racing to her side.

* * *

Mulder stood in his dark cell, he had been left alone since Samantha joyously left. He had just made up his mind to risk it and contact Scully via the crystal when the door opened.

Samantha stood there glowering, "Damn her brother. She beats me every time, but this time she won't be so lucky." Samantha walked out and slammed the door behind her. Mulder stood there uneasily, fighting the uneasy feeling rising in the pit of his stomach.

**Sorry it's so short. Please R&R, my muse needs the inspiration sometimes.**


	10. Chapter 10

Samantha stood there, glowering at Krycek, who stood behind his desk, watching her, slightly amused at her mood. "What's so different between her and me anyway? I'M supposed to be the best, the conspirators' brain child, the pride and joy of the Project. And what do they do? They take it away and give it to HER!" She kicked the wastebasket across the room.

She stalked across the room and stood next to Alex's desk , looking at him as though she was expecting him to solve her problems. "We all have our bad days Sam. Look at me, I was once at the top of the heap too, and look at me now. I'm the low man on the totem pole. Spender has everyone watching every move that I make."

"I should've been able to beat her though Alex." Samantha sighed and leaned against his desk.

Walking around the corner of the desk he wrapped his arms around her. "It'll all work out Sam, you'll see. Besides who better than us to bring down the dream team of Mulder and Scully?"

"There is no one."

Alex smiled, "Exactly. Now don't worry my love, no matter how strong she ends up being you'll beat her."

* * *

Mulder was leaning against the cold wall of his cell. His attempts to contact Scully were proving to be futile, causing his frustration to grow by the minute. Suddenly the door opened, admitting a figure, and a lot of bright light.

"Who's in here?"

Mulder recognized the voice, "Ana it's me, Mulder."

"What the hell are you doing here?"

"I could ask the same thing of you."

Ana rushed over, helping Mulder to his feet. "I have to at least look as though I'm still loyal to these people. They can't know my loyalties lie with Dana, you and everyone else like her."

"Speaking of Scully, have you heard from her recently?"

"No. Haven't you've been able to contact her using the crystal?"

"No. I'm growing worried, Samantha hit them both pretty hard."

"Them both?"

"Scully and Sapphire."

"Sapphire is _alive_? But how can that be?"

"What do you mean?"

"You see Mulder, Sapphire and Dana's friendship goes back to when this area of the Project began in it's current phase. There are what They call prototypes from before Dana and Sapphire's time here, but They don't count them as successes."

"Why not?"

"These people are to the modern world what Frankenstein's monster was to his. They don't fit in, they look as though they've been mutated. Extra eyes, animal body parts, it was almost as if They were trying to see what could improve the human body, by adding whatever was thought of."

"So what does this have to do with what happened to Sapphire?"

"Oh yes. You see Mulder, Dana knew she was to become a doctor and assist you on the X-files when she was about sixteen. That day I've never seen her so upset. Samantha 'flipped out', I believe that was how Dana put it when we calmed her down enough to tell us some of what took place. Samantha attacked Sapphire while myself and her father was discussing her new 'assignment' with Dana. I'm not sure what happened after that, she never did tell me, only that she was crying her eyes out when we found her huddled in a corner almost an hour later."

"You thought Sapphire died."

"Of course. When it comes to these children, now adults, Samantha was supposed to be the strongest."

A shadow moved out in the corridor, Ana looked up in alarm. "I'll be back later tonight, and get you out of here. In the meantime I have to play loyal subject to these bimbos."

Mulder smiled at her. "How did you get in here anyway?"

"I have almost top level clearance. That's why everyone left us alone for so long." Ana walked toward the door. "I suggest you rest as much as possible, we may have a long night ahead." She paused in the doorway, "And Mulder, Dana vowed never to spy on you, and to help you search for your sister."

Mulder watched her leave, sliding to the floor again. _Even young my Scully was loyal, innocent, and pure. _Closing his eyes he fell asleep leaning against his wall.


	11. Chapter 11

"Emily!" Scully raced through the corridor, trying to shout over the alarm that blared throughout the underground base. "EMILY!"

Sapphire came running out from the next corridor. "Dana! What's going on?" she yelled.

"I don't know! Have you seen Emily?"

"No!"

"I have to find her!" Scully took off down the corridor. "Dana, come back!"

"Sapphire!"

She turned to find Leki racing up to her. "We have to get out of here! They set this compound to self-destruct."

"I can't leave without Dana!"

"Where is she?"

"She went to find Emily!"

"_Two minutes to self-destruct."_

"There's no time to try to find them Sapphire!"

"We have to try!"

"_Two minutes and thirty seconds to self-destruct."_

Leki pulled at Sapphire's arm. "Sapphire, come on! She'll find a way out!"

Sapphire reluctantly allowed herself to be pulled in the opposite direction that Dana had gone. Leki pulled her left and right, and Sapphire let her. If someone were to ask her how she escaped the compound she wouldn't even be able to tell them. All her thoughts were of her best friend, and her hope that she would somehow make it out okay. _'Come on Dana come on. You can make it. You always do, besides Mulder would kill me if you didn't.'_

There was no response.

"_One minute to self-destruct."_

Leki pulled her out an iron door, and out into the field that surrounded the compound. They ran until Leki decided they were a safe distance from any blast. They stood there, Sapphire holding onto Leki for dear life. "Come on Dana. Come on." She the words repeated over and over.

* * *

Samantha and Kryeck opened the door, interrupting Mulder's nap. They both were smiling gleefully. Mulder opened his eyes a crack, trying to adjust his eyes to light again.

"Come along brother, we have something we would like you to see."

Kryeck pulled Mulder to his feet, and pushed him past Samantha into the hall. "What's going on?" Mulder asked as Samantha walked past him to lead them wherever they were going. His 'sister' turned around and punched him in the gut- hard. Mulder crumpled to the ground only to be brought back upright again by Krycek.

"Shut-up brother. You really must learn to mind your place among us superior beings."

Kryeck pushed him again, and he was lead into a side room on the same corridor. Inside there were monitors lining the walls, all of which were showing the same deserted building from different angles."

"Sit!"

Mulder did as he was told, his stomach was still hurting from earlier. "You see these monitors brother?"

Mulder nodded, the feeling of dread rise in his stomach again. "It is the compound where I met that goodie-two-shoes and Sapphire. It was where I grew up. We just realized some of the rebels are using it as a base, and Dana and Sapphire are among them. In less than a minute, the base will self-destruct. Hopefully taking their lives with it."

She looked at the monitors happily. "Or just Dana's, I'd be just as happy to be rid of just her."

Mulder tried to look away so he wouldn't have to see Scully die. Kryeck turned his head and held it there to force him watch.

"Thirty seconds ... Twenty ... Fifteen ..." Samantha's voice got more joy in it with each number.

Time passed slowly for Mulder, for some reason he couldn't take his eyes off the screen. It was almost if by watching he could will Scully to get out, and live. "Ten seconds... five..."

All the screens lit up like high noon, then went dark. Mulder finally shut his eyes, fighting back the tears. "Everything's gone ma'am." An emotionless voice said in the radio.

Samantha looked gleeful. "I think my brother has seen enough Alex, take him back to his cell."

* * *

At the compound Sapphire dropped to her knees. They were gone in a flash of light. Nothing was left except burning ruins. _'Daaaaana, Emilllly!'_ Her mind wailed. 


	12. Chapter 12

**Chapter 12**

**Thanks for all the great reviews. MSR ahead. Before we continue I'll give you the key to the telepathic communication coming up too. **

**_italics- _Scully **

**-_italics- -_Mulder**

**_:italics:- _Sapphire **

**'Thought'- Ana**

**_ITALICS _Reika or Eva**

**Without further delay, here's our story.**

Sapphire and Leki clutched each other, staring at the ruins. There was only a part of the structure still standing in the center of the crater left behind by the blast. Darkness began to fall over them and the woods surrounding them. Tears streamed down Sapphire's face, both Dana and Emily were ... gone. A black helicopter flew over the ruins.

"You bastards! Come back here! Cowards, you killed them! You killed them!" Sapphire began to run after the helicopter, towards the crater.

"Sapphire!" Leki ran after her, Sapphire was looking up at the helicopter, not looking at the ground unlike she. Two figures were emerging from the area of the compound that was still standing. "Sapphire!"

Sapphire whirled around. "What!"

"Look behind you!"

"But..." The helicopter was disappearing over the tree tops and so was her chance for revenge.

"Just look!"

For the first time in her life Sapphire finally listened someone, and didn't act boldly. She whirled around and stared at the crater. "I don't see anything."

Leki came up behind her. "I saw to figures down there."

"Leki, if you mean Dana and Emily are still alive we may have to have your head examined because I think your time below has gotten to you."

"Just watch. I'm sure of what I saw."

So they watched, and waited. They stood there for about a half-an-hour, finally the two figures made it up from the bottom of the crater.

"We made it mommy!" the smallest one squealed.

"Yes we did Emmy, yes we did."

Sapphire recognized the second voice. "Dana!" She ran up and threw herself at her friend. "Don't you ever do that to me again dammit!"

"I'll try."

Leki asked softly. "Are the two of you all right?"

"We're fine, a little bruised and I have a few cuts but we're fine." Dana pulled Emily closer to her as Sapphire finally let her go.

"What now?" asked Sapphire looking from Dana to Leki.

"We go find Samantha that's what. And end this madness."

* * *

_Syndicate Compound_

Mulder leaned up against his wall, he hadn't eaten in 12 hours, but he didn't care. Scully was gone, and she would never know how much she meant to him. Mulder felt the tears threaten to fall, it was all he had the energy left to do. He had spent to first six hours since Krycek had thrown him in the cell, yelling himself hoarse at the guards outside who just laughed at Scully's death.

The cell door opened and Ana entered. "Mulder it's time to go."

"What's the point?" He turned away from her.

"What's the point? Don't you want to see Dana again?"

Mulder jumped up and pulled out his gun, aiming at her. "Are you people trying to rub this in my face! Scully is dead. Scully is ..."

Ana calmly looked down the gun barrel. "Samantha must be slipping." She equally calm to the grieving man. "What are you talking about? Dana is alive. I've spoken to Sapphire who confirms it."

Mulder just gaped at her. His mouth moved up and down, the words wouldn't come. "Come on." She pulled him out of the cell, and past the unconscious guards.

* * *

_Unknown forest near ruined compound_

Sapphire lead the way through the forest followed by Dana who was giving Emily a piggy-back ride. Leki brought up the rear, both Sapphire and she were holding futuristic looking guns. The two women looked all around them, determined to get Dana and Emily safely to Mulder.

"If we're going to bring Them down, we're going to need help." said Sapphire.

The other two nodded. "Look ahead of us." whispered Dana, easing Emily down and taking out her knife. "Who's there?" Shouted Leki.

"Reika and Eva."

Sapphire and Dana slightly dropped their guards. "How do we know you're you?"

"Come on D, who else would know about "Red Devil"!" an exasperated voice said.

"Well come on out then." Demanded Sapphire.

Two identical women walked out from a clump of trees. Both were tall and had long, dark brown hair and light brown eyes. "I see you were expecting trouble." said Reika glancing at the weapons.

"How did you get here?" asked Sapphire.

"We heard what was going on through the grapevine, so we took the bikes and brought them to Hawks Nest." Said Eva, handing Dana and Sapphire some keys.

"We can't take those old things, I have Emily."

Reika waved it off. "We took it to someone who actually knows what he's doing and he fixed them up to code, and made yours to fit Emily."

"Let me guess the grapevine?" asked Sapphire.

"Yup."

"Well it's a good thing I told Ana and Mulder to meet us in Hawks Nest."

Emily was walking behind Leki, Sapphire, and Eva with Reika. Eva calculated that they could make Hawks Nest and the motel by at least nightfall with a quick stop at the town's only gas station for the bikes.

"How did you all meet?" asked Leki.

"We were put in the same group when they "upgraded" us and trained us for their army." said Dana, glancing around them.

"And when you go through that hell, you have friends for life." said Eva bitterly.

"At least when you went through it you had each other. When this area of the project began we were separated, it was only until They thought we were submissive and believed all the lies were we allowed out of our cells and able to see each other."

"They did that to me once." commented Dana softly causing the other three to look at her in alarm. She glanced backwards to make sure Emily and Reika were preoccupied before continuing. "It's Their way of breaking insubordinate "children". They didn't like it that I was being good and not helping Mulder."

"So we're their "children". How cute." said Eva. "They sure don't treat us like we're their kids."

'**Mulder will you please stay clam?'**

_-I'm trying but she's right in front of us!-_

"What in the world was that?" demanded Reika from behind them.

"Ana and Mulder." said Sapphire.

"Where are they?" asked Leki.

"I couldn't tell." said Dana, trying to keep the panic out of her voice.

* * *

_Near Hawk's Nest, West Virginia_

Ana and Mulder were staring out the front windshield. In front of them stood Samantha in the middle of the road.

"Tsk, tsk. What do we have here?"


	13. Reunion

**Chapter 13**

**A/N:**

**Hawk's Nest, West Virginia is a real place, but when I was there I was just passing through so I'm not sure the description is accurate sorry. I apologize also for not putting spoilers in the first chapter, I'm kinda new at this and didn't think of it so I'll put them here. The spoilers are: Emily, Ascension, One Breath, Emily, and Christmas Carol. This story takes place during the 7th season. Again sorry.**

They quickened their pace, trying to hurry and get to Mulder and Ana before Samantha did something to them. "Why are we walking for Christ's sake? Teleporting is faster." Growled Dana.

"If we do then the Syndicate can track us. Reika and I noticed one of their search drones overhead after we reappeared." said Eva.

"While we pass the time, I have a question for you D. Do you love Mulder.?" asked Reika from behind them.

"We're friends, nothing more."

"I see the look in your eyes every time we talk about him."

Dana's face turned as red as her hair.

"Yeah she does." chimed Sapphire.

"Fine, fine. I do, but it's wasted because he goes for women who look like Eva and Reika, not me. Besides even if he did, it's wasted because the Bureau and the Syndicate wouldn't allow it. We'd be separated in an instant and God knows what would happen to either Mulder or I." With that she scooped Emily up in her arms, and stormed off ahead of them.

* * *

_Near Hawks Nest, West Virginia_

Samantha walked slowly towards the car. Ana was trying to drive away but Samantha had taken over the controls of the car.

"Drive away!" yelled Mulder.

"I can't, she's interfering with the car!"

"How did she find us anyway?"

"How should I know! I have no idea what she or Dana can do!"

Samantha choose that moment to leap on the hood of their car, and slammed her fist in the center causing a huge hole in the engine.

* * *

_Hawk's Nest, West Virginia_

The group of women walked into the gas station parking lot, promptly heading to two parking spaces that held four motorcycles. "Welcome to Hawk's Nest, West Virginia." said Reika, leading them to the small town's only gas station. Four motorcycles were parked in two parking spaces towards the back of the gas station parking lot. "They look like new." said Sapphire in awe.

"As new as you can get for these old things." joked Dana looking at her own dubbed 'Red Devil'.

"What in the world?" they heard someone yell behind them. They all turned around to see a car limping into the gas station, smoke pouring from a huge hole in it's engine. It had the entire gas station's attention, or at least the most of them. Emily's attention was still focused on her mom's motorcycle.

"Why does this have Samantha's name all over it?" asked Eva darkly.

"Because she's heartless." said Leki.

"She's a mindless minion." added Reika.

The front doors of the car opened, Mulder and Ana got out to survey the damage. "Mulder!" called Scully. He looked up in shock. "Scully!" Scully launched herself into a run, and threw herself into his arms, wrapping her arms tightly around him.

"And she says there's nothing there." murmured Reika to her friends.

"What happened to the car?" asked Sapphire looking at the crowd that stayed a safe distance away.

"Samantha." said Mulder, pulling slightly away from Scully, but he kept his arm around her. "The funny thing is she didn't do anything else."

"How did you get here?" asked Leki, gesturing towards the car. "It doesn't look safe."

"Very slowly." said Ana wiping her brow with her forearm. "It's fine except if it's running."

There was a quiet sigh of relief among the crowd, and they began to return to their normal activities. Since they weren't the center of attention Emily walked over. Scully happily picked her up. "Mommy!"

"Uhh ... Scully, who's this?" Mulder was puzzled, hadn't this little girl died two years ago?

"This is Emily; Mulder."

"Didn't..."

"That was a clone Mulder."

* * *

_Syndicate Compound_

Samantha strode angrily down the corridor, she had been about to kill her brother when she got the order to withdraw. CSM saw her coming and tried to run. "I don't think so." She smirked, lifting him up off the ground with her hand around his throat.

"Samantha-" Her hand around his throat tightened, making it harder to breath. "We had to call you back. Skinner was putting pressure on us, he was going to expose us if you didn't back off." Her grip tightened even more.

"I don't care, she needs to pay."

CSM was getting desperate, as much as he wanted to see the X-files end and the Project succeed, he valued his life more. "Samantha. This doesn't mean you won't get your chance. As soon as Skinner backs off, I promise you."

She thought over this for a few moments and dropped him to the ground. "Fine, I'll back off. But the second, the **second**, he backs off. I'm there." CSM tried to hide his relieved look, but Samantha noticed. "This time I think I'll kill her. The clone of my her and my brother's kid didn't do the trick when I created it to be destroyed in order to destroy her. She didn't do what I expected, either leave the X-files, or do us all a favor and kill herself. No. She kept working."

Turning on her heel she stalked off. CSM watched her go knowing full well she would keep her word. The hatred for some reason ran deep between these two "children". The Syndicate had played a dangerous game when they made someone as strong as Samantha, luckily she was loyal to them. Then there was Dana, who was stronger and not loyal, she had never been meant to be stronger, but there were sloppy mistakes that they couldn't fix. When these two met in battle it would be fierce, and CSM had a feeling Dana would be the victor. The question remained though, was the world ready to see this meeting take place?


	14. Mulder's Role

**Chapter 14**

**Sorry it took so long with the update, I lost the notebook I had the rest of this story in. So I had to rewrite the whole ending, so now the only dilemma is making Samantha and Scully's fight live up to all the hype it's been getting all story long. Anyway enough with my babbling, enjoy the chapters and Happy 2006!**

With Samantha in the area the group decided to use the bikes to get out of there as soon as possible. Eva rode with Ana and Reika with Leki in the front; followed by Scully and Emily, and next to them were Sapphire and Mulder.

_-Where are we going?-_

_TO DANA'S HOUSE, THE ONE THE SYNDICATE GAVE HER IN THE HAMPTONS. _Eva smiled.

_-What?-_

_Mulder, I was once their top operative, They felt they had to repay me somehow. _

_-What about your apartment in DC?-_

Reika laughed mentally. _MULDER, MULDER, MULDER. DANA EARNED THAT PLACE ALL BY HERSELF. AFTER SHE STARTED HELPING YOU AGAINST THEIR WISHES THEY TOOK THE HAMPTONS PLACE AWAY._

_But by then I all ready had the apartment._

Mulder just shook his head in disbelief, it still all still seemed like an elaborate dream that his mind almost couldn't handle. First he learned his beloved partner was superhuman, and part of the organization they both seemed to despise. Then he learned that for years she had worked against them by being among them, and hated everything They stood for. Now he was learning she once had a place where only the richest people lived.

_IT'S SAFE TO TELEPORT NOW. _Eva said suddenly.

_-Wait what's wrong with riding?- _demanded Mulder.

_It's way too slow Mulder, we want to get there before nightfall. What's the matter nervous? _Mulder could hear Scully was enjoying every moment of this.

-_Of course not!- _His voice said otherwise.

_:Don't worry we do this all the time Just hang on tight.:_

_OKAY, EVERYONE READY?_ Eva asked, the women mentally nodded while Mulder panicked. _ONE THREE. 3...2...1._

Instantaneously Mulder felt himself be jerked forward. Air rushed past them, Mulder felt as though he was going to be sick; almost losing his stomach on a rather sharp corner. Lights flashed around the group as they were hurled and whipped through inter-dimensionalspace. At last they came to a sudden stop, a huge mansion materializing seemingly out of nowhere.

Mulder leaned back against the bike trying to allow the rest of himself to catch up. Scully looked at him, torn between amusement and worry picking Emily out of the seat and carrying her towards the house talking quietly with Ana. Leki followed them up to the house soon after leaving Mulder alone with the girls.

Sapphire pulled on Mulder's arms. "It gets better if you walk."

Mulder just groaned. "Never again."

The women looked at him amused. "You remind me of Spender when he found his office full of frogs and frog spawn." Reika laughed hysterically. "Little did he know Dana did it."

They began to walk towards the large deck overlooking the ocean. "Scully did what!"

"We were thirteen, and Spender is a pain no matter when you meet him, so that's how we retaliated." Eva said shrugging.

Emily appeared clad in a bathing suit. "Mommy says we're going swimming so come on!"

The three woman laughed at her softly, leaving Mulder alone. Ana joined him laughing as the girls raced towards the water, Leki following at a safe distance. "What is it?" asked Mulder.

"The way they act, you'd think they were teens again, giving the Syndicate a headache. You see Mulder, with all their genius ways of keeping themselves a secret Spender and the others had no idea how to control teenagers."

Mulder laughed as he thought back to Scully and the frogs in Spender's office. Scully turned briefly before plunging into the surf. "Come on Mulder, Ana! You're missing all the fun!"

"I've honestly never seen her so happy. Her childhood was full of continuous "improvements", full of pain, and laughter was rare, despite having this group around her. Even life at home was full of arguments in between the happy times." Ana looked thoughtful for a moment. "You know it wasn't until she met you did she seem truly happy."

"Really?"

Ana nodded. "She was openly fighting the people she hated, with the man she loved. A feeling that I now see is mutal."

Mulder's face reddened. "Wha..what are you talking about."

"Love."

"Is it that obvious?"

"I'd say so. Perhaps its what gave Samantha the idea to make you Emily's father. You'll recall an incident that you have vague recollections of at Elis Air Force Base."

"So you mean..."

"Exactly."

Mulder paused thoughtfully, slightly disturbed at how matter of factly Ana said all of this. "No Mulder Dana didn't know all this. In fact up to few days ago Emily's father was still unknown and Emily was believed to be dead."

"What I don't get is what is so dangerous about Samantha and Scully meeting in any sort of fight. So far all I've seen is that Scully's just like the rest of them."

"Yes, but you've only seen the tip of the iceberg I'm afraid. There's a lot more here than meets the eye, some even they don't know about. And a lot that Dana doesn't know. You all ready know that the changes made to Dana as an adult were unintentional, but it still happened and now we have to deal with it."

"Ana you're going around the question, just answer it."

"The truth is Mulder that these "children" of the Syndicate all have the advanced abilities that Dana and Samantha can control hidden within them, dormant. All their abilities are triggered by strong thought or emotion. If given the power Dana and Samantha have they could call upon nature itself to aide them in battle with no control over what it destroys in order to do so. That's why the Syndicate decided that the only child who should be able to do these things should be loyal to them, and Samantha was chosen. Making her loyal means she would protect them."

"But they gave them to Scully as well."

"By accident if you recall Mulder.They gave her the abilities as punishment, and they were trying to do whatever to hurt her regardless of the results. And the idiots did another dumb thing, they made it so her abilities would grow, and now she's stronger than your sister."

"So if these two meet..."

"Their anger towards one another could destroy the entire world."

Mulder stood there dumbstruck, the information slowing sinking in. Ana seemed to read his thoughts. "I don't not know why they hate one another so."

Emily ran up towards them. "Come on, play with us!"

Mulder smiled at her. "Tell you whatyou go back and play with your mommy and her friends, I'll go get my suit on and go join you."

"Okay Daddy!" The little girlskipped off.

Mulder turned to go inside. "Mulder." He turned and faced Ana. "Confess your love to Dana. She will need your help to beat your sister. And the world will need you beside Dana if it is to survive. You alone can help her control her feelings toward Samantha."

And with that Ana walked past him and down the steps, leaving Mulder bewildered. Sighing at how vague the woman could be Mulder headed into the house to join the girls in the water.


End file.
